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Showing papers on "Glycome published in 2018"


Journal ArticleDOI
TL;DR: The Immunoglobulin G (IgG) glycome is well known for its heterogeneity and shows a significant degree of variation within populations, making it an excellent biomarker of a person's general health state and a promising add-on to improve existing disease biomarkers.

257 citations


Journal ArticleDOI
TL;DR: The field of glycan-directed CAR-T cells is discussed and the different classes of antibodies specific for glyCAN-targeting are reviewed, including the generation of high affinity O-glycopeptide antibodies.
Abstract: Cancer immunotherapy is rapidly advancing in the treatment of a variety of hematopoietic cancers, including pediatric acute lymphoblastic leukemia and diffuse large B cell lymphoma, with chimeric antigen receptor (CAR)-T cells. CARs are genetically encoded artificial T cell receptors that combine the antigen specificity of an antibody with the machinery of T cell activation. However, implementation of CAR technology in the treatment of solid tumors has been progressing much slower. Solid tumors are characterized by a number of challenges that need to be overcome, including cellular heterogeneity, immunosuppressive tumor microenvironment (TME), and, in particular, few known cancer-specific targets. Post-translational modifications that differentially occur in malignant cells generate valid cell surface, cancer-specific targets for CAR-T cells. We previously demonstrated that CAR-T cells targeting an aberrant O-glycosylation of MUC1, a common cancer marker associated with changes in cell adhesion, tumor growth and poor prognosis, could control malignant growth in mouse models. Here, we discuss the field of glycan-directed CAR-T cells and review the different classes of antibodies specific for glycan-targeting, including the generation of high affinity O-glycopeptide antibodies. Finally, we discuss historic and recently investigated glycan targets for CAR-T cells and provide our perspective on how targeting the tumor glycoproteome and/or glycome will improve CAR-T immunotherapy.

66 citations


Journal ArticleDOI
TL;DR: A library of validated high-efficiency gRNA designs suitable for individual and combinatorial targeting of the human glycosyltransferase genome together with a global view of the predicted functions of human gly cosyltransferases to facilitate and guide gene targeting strategies in studies of thehuman glycome are presented.
Abstract: Over 200 glycosyltransferases are involved in the orchestration of the biosynthesis of the human glycome, which is comprised of all glycan structures found on different glycoconjugates in cells. The glycome is vast, and despite advancements in analytic strategies it continues to be difficult to decipher biological roles of glycans with respect to specific glycan structures, type of glycoconjugate, particular glycoproteins, and distinct glycosites on proteins. In contrast to this, the number of glycosyltransferase genes involved in the biosynthesis of the human glycome is manageable, and the biosynthetic roles of most of these enzymes are defined or can be predicted with reasonable confidence. Thus, with the availability of the facile CRISPR/Cas9 gene editing tool it now seems easier to approach investigation of the functions of the glycome through genetic dissection of biosynthetic pathways, rather than by direct glycan analysis. However, obstacles still remain with design and validation of efficient gene targeting constructs, as well as with the interpretation of results from gene targeting and the translation of gene function to glycan structures. This is especially true for glycosylation steps covered by isoenzyme gene families. Here, we present a library of validated high-efficiency gRNA designs suitable for individual and combinatorial targeting of the human glycosyltransferase genome together with a global view of the predicted functions of human glycosyltransferases to facilitate and guide gene targeting strategies in studies of the human glycome.

63 citations


Journal ArticleDOI
TL;DR: Comprehensive glycome profiling of immunoglobulin G (IgG) in 95 strains of mice from the Collaborative Cross genetics resource reveals the extent and variability of IgG glycosylation in vivo.
Abstract: Immunoglobulin G (IgG) glycosylation is essential for function of the immune system, but the genetic and environmental factors that underlie its inter-individual variability are not well defined. The Collaborative Cross (CC) genetic resource harnesses over 90% of the common genetic variation of the mouse. By analyzing the IgG glycome composition of 95 CC strains, we made several important observations: (i) glycome variation between mouse strains was higher than between individual humans, despite all mice having the same environmental influences; (ii) five genetic loci were found to be associated with murine IgG glycosylation; (iii) variants outside traditional glycosylation site motifs affected glycome variation; (iv) bisecting N-acetylglucosamine (GlcNAc) was produced by several strains although most previous studies have reported the absence of glycans containing the bisecting GlcNAc on murine IgGs; and (v) common laboratory mouse strains are not optimal animal models for studying effects of glycosylation on IgG function.

58 citations


Journal ArticleDOI
TL;DR: The findings indicated that loss of galactose and sialic acid, as well as addition of bisecting GlcNAc, might involve in pro- or anti-inflammatory IgG functionality and further contribute to the pathogenesis of IS.
Abstract: Glycosylation significantly affects protein structure and function and thus participates in multiple physiologic and pathologic processes. Studies demonstrated that immunoglobulin G (IgG) N-glycosylation associates with the risk factors of ischemic stroke (IS), such as aging, obesity, dyslipidemia, type 2 diabetes, and hypertension. The study aimed to investigate the association between IgG N-glycosylation and IS in a Chinese population. IgG glycome composition in patients with IS (n = 78) and cerebral arterial stenosis (CAS) (n = 75) and controls (n = 77) were analyzed by ultra-performance liquid chromatography. Eleven initial glycans and 10 derived glycans in IgG glycome representing galactosylation, sialylation, and bisecting GlcNAc significantly differed between IS patients and CAS and healthy controls after controlling for gender, age, obesity, diabetes, hypertension, and dyslipidemia. Logistic regression models incorporating IgG glycan traits were able to distinguish IS from CAS (area under receiver–operator characteristic curves (AUC), 0.802; 95% confidence interval (CI), 0.732–0.872) and controls (AUC, 0.740; 95% CI, 0.661–0.819). The canonical correlation analysis indicated that initial N-glycan structures are significantly correlated with inflammation markers (r = 0.566, p < 0.001). Our findings indicated that loss of galactose and sialic acid, as well as addition of bisecting GlcNAc, might involve in pro- or anti-inflammatory IgG functionality and further contribute to the pathogenesis of IS. IgG glycan profiles may be developed as clinical useful biomarkers for chronic disease in the future.

57 citations


Journal ArticleDOI
TL;DR: Glyopeptide analyses provided insights into the glycoprotein candidates possibly associated with the observed N-glycan changes, with glycoproteins associated with binding events being the most frequently identified class.
Abstract: The glycome of one of the largest and most exposed human organs, the skin, as well as glycan changes associated with non-melanoma skin cancers have not been studied in detail to date. Skin cancers such as basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are among the most frequent types of cancers with rising incidence rates in the aging population. We investigated the healthy human skin N- and O-glycome and its changes associated with BCC and SCC. Matched patient samples were obtained from frozen biopsy and formalin-fixed paraffin-embedded tissue samples for glycomics analyses using two complementary glycomics approaches: porous graphitized carbon nano-liquid chromatography electro spray ionization tandem mass spectrometry and capillary gel electrophoresis with laser induced fluorescence detection. The human skin N-glycome is dominated by complex type N-glycans that exhibit almost similar levels of α2-3 and α2-6 sialylation. Fucose is attached exclusively to the N-glycan core. Core 1 and core 2 type O-glycans carried up to three sialic acid residues. An increase of oligomannose type N-glycans and core 2 type O-glycans was observed in BCC and SCC, while α2-3 sialylation levels were decreased in SCC but not in BCC. Furthermore, glycopeptide analyses provided insights into the glycoprotein candidates possibly associated with the observed N-glycan changes, with glycoproteins associated with binding events being the most frequently identified class.

40 citations


Journal ArticleDOI
TL;DR: The detection of mammalian (tissue) lectins and the emerging evidence for intimate molecular recognition between this class of receptors and their (glycoconjugate) counterreceptors substantiate that understanding the rules of the sugar code is presently a major challenge.
Abstract: About 60 years ago, the efforts to identify blood group-specific haemagglutinins in plant extracts by broad-scale testing were beginning to make a large panel of these proteins available as laboratory tools. Their ability to ‘read’ cell surface signals like antibodies do was the reason for W. C. Boyd to call them lectins, from Latin legere (to read). These proteins turned out to be as widely present in nature as glycans (polysaccharides or carbohydrate chains of cellular glycoconjugates) are. Since carbohydrates have the virtue to facilitate high-density coding in a minimum of space and lectins (initially mostly from plants called phytohaemagglutinins) turned out to be receptors for glycans, their pairing made many applications possible. Most prominently, these proteins were instrumental to map glycome complexity and sites of product generation during glycan assembly in the cell. The detection of mammalian (tissue) lectins and the emerging evidence for intimate molecular recognition between this class of receptors and their (glycoconjugate) counterreceptors substantiate that understanding the rules of the sugar code is presently a major challenge.

39 citations


Journal ArticleDOI
TL;DR: The neoglycolipid technology is the basis of a state‐of‐the‐art oligosaccharide microarray system, which is offered for screening analyses to the broad scientific community and its power in pinpointing and isolating naturally occurring ligands for glycan‐binding proteins (GBPs) within glycan populations is reviewed.

37 citations


Journal ArticleDOI
TL;DR: Sialic acid distribution was quantified by LC-MS/MS and the number of sialylated glycoforms increases at sites nearest to the transmembrane domain.
Abstract: Given that unnatural sugar expression is metabolically achieved, the kinetics and disposition of incorporation can lend insight into the temporal and localization preferences of sialylation across the cell surface. However, common detection schemes lack the ability to detail the molecular diversity and distribution of target moieties. Here we employed a mass spectrometric approach to trace the placement of azido sialic acids on membrane glycoconjugates, which revealed substantial variations in incorporation efficiencies between N-/O-glycans, glycosites, and glycosphingolipids. To further explore the propensity for sialylation, we subsequently mapped the native glycome of model epithelial cell surfaces and illustrate that while glycosylation sites span broadly across the extracellular region, a higher number of heterogeneous glycoforms occur on sialylated sites closest to the transmembrane domain. Beyond imaging techniques, this integrative approach provides unprecedented details about the frequency and structure-specific distribution of cell surface sialylation, a critical feature that regulates cellular interactions and homeostatic pathways.

37 citations


Journal ArticleDOI
TL;DR: This review aimed to provide a glimpse into the evolution of Sia and their implications to xenotransplantation.
Abstract: All living cells are covered with a dense "sugar-coat" of carbohydrate chains (glycans) conjugated to proteins and lipids. The cell surface glycome is determined by a non-template driven process related to the collection of enzymes that assemble glycans in a sequential manner. In mammals, many of these glycans are topped with sialic acids (Sia), a large family of acidic sugars. The "Sialome" is highly diverse owing to various Sia types, linkage to underlying glycans, range of carriers, and complex spatial organization. Presented at the front of cells, Sia play a major role in immunity and recognition of "self" versus "non-self," largely mediated by the siglecs family of Sia-binding host receptors. Albeit many mammalian pathogens have evolved to hijack this recognition system to avoid host immune attack, presenting a fascinating host-pathogen evolutionary arms race. Similarly, cancer cells exploit Sia for their own survival and propagation. As part of this ongoing fitness, humans lost the ability to synthesize the Sia type N-glycolylneuraminic acid (Neu5Gc), in contrast to other mammals. While this loss had provided an advantage against certain pathogens, humans are continuously exposed to Neu5Gc through mammalian-derived diet (eg, red meat), consequently generating a complex immune response against it. Circulating anti-Neu5Gc antibodies together with Neu5Gc on some human tissues mediate chronic inflammation "xenosialitis" that exacerbate various human diseases (eg, cancer and atherosclerosis). Similarly, Neu5Gc-containing xenografts are exposed to human anti-Neu5Gc antibodies with implications to sustainability. This review aimed to provide a glimpse into the evolution of Sia and their implications to xenotransplantation.

33 citations


Journal ArticleDOI
TL;DR: Traditional PNGase F and A release may be insufficient for release of the more highly core-modified N-glycans, especially those occurring in C. elegans, but novel enzymes can compete against chemical methods in terms of safety, ease of cleanup, and quality of resulting glycomic data.
Abstract: Despite years of research, the glycome of the model nematode Caenorhabditis elegans is still not fully understood. Certainly, data over the years have indicated that this organism synthesizes unusu...

Journal ArticleDOI
TL;DR: It is demonstrated that the characteristic glycan signature of hiPSCs are retained by EVs derived from them, indicating that the EV glycome could be novel targets for the identification and characterization of stem cells for use in regenerative medicine.
Abstract: Glycans are one of the major building blocks of extracellular vesicles (EVs). However, their roles and applications have not been completely explored. Here, we analyzed the glycome of EVs derived from human induced pluripotent stem cells (hiPSCs) using high-density lectin microarray. The glycan profiles of hiPSC-derived EVs were different from those of non-hiPSC-derived EVs. Moreover, rBC2LCN that shows specific binding to hiPSCs, showed strong specificity for hiPSC-derived EVs but not non-hiPSCs-derived EVs. Further, other hiPSC-specific probes, such as anti-TRA-1-60, anti-SSEA4, and anti-R-10G, exhibited specific, but weaker binding to hiPSC-derived EVs than rBC2LCN. We then developed a sandwich assay using rBC2LCN and a phosphatidylserine receptor, Tim4, to specifically detect hiPSC-derived EVs. The Tim4-rBC2LCN sandwich assay allowed for specific detection of hiPSC-derived EVs but not non-hiPSC-derived EVs, indicating that rBC2LCN could also be used for the specific detection of hiPSC-derived EVs. Together, our findings demonstrate that the characteristic glycan signature of hiPSCs are retained by EVs derived from them. The EV glycome could be novel targets for the identification and characterization of stem cells for use in regenerative medicine.

Journal ArticleDOI
TL;DR: In this article, a targeted microarray approach is proposed for O-glycome beam search that is both robust and efficient for ligand-discovery, which simplifies the complex Oglycome profile and achieves facile chromatographic resolution by arraying Oglycans as branches.

Journal ArticleDOI
TL;DR: A novel isotope labeling approach termed Isotope-Cellular O-glycome Reporter Amplification (ICORA), which enables ~100-1000-fold enhanced sensitivity and increased throughput compared to traditional O- Glycomics and is validated with model cell lines and used to define alterations in the O- glycome in colorectal cancer.
Abstract: Mucin-type O-glycans decorate >80% of secretory and cell surface proteins and contribute to health and disease. However, dynamic alterations in the O-glycome are poorly understood because current O-glycomic methodologies are not sufficiently sensitive nor quantitative. Here we describe a novel isotope labeling approach termed Isotope-Cellular O-glycome Reporter Amplification (ICORA) to amplify and analyze the O-glycome from cells. In this approach, cells are incubated with Ac3GalNAc-Bn (Ac3GalNAc-[1H7]Bn) or a heavy labeled Ac3GalNAc-BnD7 (Ac3GalNAc-[2D7]Bn) O-glycan precursor (7 Da mass difference), which enters cells and upon de-esterification is modified by Golgi enzymes to generate Bn-O-glycans secreted into the culture media. After recovery, heavy and light Bn-O-glycans from two separate conditions are mixed, analyzed by MS, and statistically interrogated for changes in O-glycan abundance using a semi-automated approach. ICORA enables ~100-1000-fold enhanced sensitivity and increased throughput compared to traditional O-glycomics. We validated ICORA with model cell lines and used it to define alterations in the O-glycome in colorectal cancer. ICORA is a useful tool to explore the dynamic regulation of the O-glycome in health and disease.

Journal ArticleDOI
TL;DR: The protocols employed in the laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species are presented.
Abstract: Protein glycosylation, the most universal and diverse post-translational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species-and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N-and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.

Journal ArticleDOI
TL;DR: Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE was developed, which used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures.

Journal ArticleDOI
TL;DR: Clinically-relevant activities of defined subsets of freshly-isolated and culture-expanded human PBMC-derived Tregs are examined to indicate that the immature Treg glycome is under unique regulation and that adult PBMCs can be an ideal source of autologous-derived therapeutic T Regs, provided that subset selection and glycan engineering are engaged to optimize both their immunomodulation and tropism for inflammatory sites.
Abstract: While human Tregs hold immense promise for immunotherapy, their biologic variability poses challenges for clinical use. Here, we examined clinically-relevant activities of defined subsets of freshly-isolated and culture-expanded human PBMC-derived Tregs. Unlike highly suppressive but plastic memory Tregs (memTreg), naive Tregs (nvTreg) exhibited the greatest proliferation, suppressive capacity after stimulation, and Treg lineage fidelity. Yet, unlike memTregs, nvTregs lack Fucosyltransferase VII and display low sLeX expression, with concomitant poor homing capacity. In vitro nvTreg expansion augmented their suppressive function, but did not alter the nvTreg sLeX-l ° w glycome. However, exofucosylation of the nvTreg surface yielded high sLeX expression, promoting endothelial adhesion and enhanced inhibition of xenogeneic aGVHD. These data indicate that the immature Treg glycome is under unique regulation and that adult PBMCs can be an ideal source of autologous-derived therapeutic Tregs, provided that subset selection and glycan engineering are engaged to optimize both their immunomodulation and tropism for inflammatory sites.

Journal ArticleDOI
TL;DR: The first detailed description of genes associated with protein glycosylation in a parasitic flatworm is provided, focusing on the genome of the liver fluke (Fasciola hepatica), which is a globally important trematode parasite of humans and their livestock.
Abstract: Glycoproteins secreted by helminth parasites are immunogenic and represent appealing components of vaccine preparations. Our poor knowledge of the pathways that mediate protein glycosylation in parasitic flatworms hinders our understanding of how proteins are synthesised and modified, and our ability to target these pathways for parasite control. Here we provide the first detailed description of genes associated with protein glycosylation in a parasitic flatworm, focusing on the genome of the liver fluke (Fasciola hepatica), which is a globally important trematode parasite of humans and their livestock. Using 190 human sequences as search queries against currently available F. hepatica genomes, we identified 149 orthologues with putative roles in sugar uptake or nucleotide sugar synthesis, and an array of glycosyltransferase and glycosidase activities required for protein N- and O-glycosylation. We found appreciable duplication within these orthologues, describing just 87 non-redundant genes when paralogues were excluded. F. hepatica lacks many of the enzymes required to produce complex N- and O-linked glycans, which explains the genomic basis for the structurally simple glycans described by F. hepatica glycomic datasets, and predicts pervasive structural simplicity in the wider glycome. These data provide a foundation for functional genomic interrogation of these pathways with the view towards novel parasite intervention strategies.

Journal ArticleDOI
TL;DR: The data strongly suggests high-mannose as a marker for secreted proteins mediating innate antiviral immunity in vaginal fluids and that drug formulation may impact this activity as reflected in the glycome.
Abstract: Glycosylated proteins (i.e., mucins, IgG) are important mediators of innate antiviral immunity in the vagina; however, our current knowledge of the role that glycan themselves play in genital immun...

Journal ArticleDOI
TL;DR: This work reports the large-scale characterization of human liver N-glycome with primary structures, where 214 unique N- glycans with unique primary structures were identified and visualized with spectrum-level false discovery rate ≤ 1% and number of best hits of 1.
Abstract: Aberrant glycosylation has been commonly observed in various physiological and pathological disorders (including cancers), and quite a few glycoproteins have been approved by the US Food and Drug Administration (FDA) as markers for early diagnosis. Each glycoprotein may have multiple glycoforms, and cancer-related ones can be only some specific glycoforms which have much higher sensitivity and specificity; for example, AFP glycoform AFP-L3 with N-glycan of 01Y(61F)41Y41M(31M41Y41L41S61M41Y41L41S is of bigger diagnostic value for hepatocellular carcinoma than total AFP (i.e., combination of all glycoforms). Mass spectrometry-based glycomics is currently the state-of-the-art instrumental analytical pipeline for high-throughput characterization of various glycoforms, where not only monosaccharide composition but also comprehensive structural information (sequence and linkage) of N-glycans are now reported thanks to our recently developed N-glycan database search engine GlySeeker. With this new capability, here, we report our large-scale characterization of human liver N-glycome with primary structures; 214 unique N-glycans with unique primary structures were identified and visualized with spectrum-level false discovery rate ≤ 1% and number of best hits of 1. The LO2 N-glycans reported here serve as a basic reference for future liver N-glycome study, and further quantitative analysis will enable characterization of differentially expressed N-glycans and discovery of more effective markers for liver and other diseases. Data are available via ProteomeXchange with identifier PXD008158.

Journal ArticleDOI
TL;DR: This review focuses on some of the technological and methodological advances in the field of glycobiology that are being deployed to lower the barrier of entry into the glycosciences, and to more fully interrogate the glycome and its function.

Journal ArticleDOI
TL;DR: Application of lectin microarrays exploiting simultaneous interaction of seminal plasma samples with multiple lectins of different sugar specificities to compare the glycomes of fertile and infertile men indicates reduced lectin reactivity associated with decreased fertility.
Abstract: We report application of lectin microarrays, exploiting simultaneous interaction of seminal plasma samples with multiple lectins of different sugar specificities to compare the glycomes of fertile and infertile men. The results indicate reduced lectin reactivity associated with decreased fertility, especially affecting oligozoospermic subjects and probably O-glycosylation. Lectin microarrays may become a potent tool for semen analysis in search of the association of glycosylation and male fertility.

Journal ArticleDOI
11 Jul 2018-PLOS ONE
TL;DR: The glycome was stable upon storage after centrifugation and aliquoting, which is an important information considering future diagnostic applications, and negatively correlated with an established glycan score for ovarian cancer, when evaluated by MALDI-TOF-MS measurement.
Abstract: Glycome modulations have been described in the onset and progression of many diseases. Thus, many studies have proposed glycans from blood glycoproteins as disease markers. Astonishingly, little effort has been given unraveling preanalytical conditions potentially influencing glycan analysis prior to blood biomarker studies. In this work, we evaluate for the first time the effect of hemolysis, storage and blood collection, but also influence of various times and temperatures between individual processing steps on the total N-glycome and on a glycan-biomarker score. Venous blood was collected from 10 healthy donors in 11 blood collection tubes with different additives, processed variously to obtain 16 preanalytical variables and N-glycans released from serum or plasma were analyzed by MALDI-TOF-MS and capillary electrophoresis coupled with fluorescence detection (CE-LIF) for the first time. Long time storage of deep frozen samples at -20°C or -80°C exerted only a minor influence on the glycome as demonstrated by CE-LIF. The N-glycome was very stable evidenced by MALDI-TOF when stored at 4°C for at least 48 hours and blood collected in tubes devoid of additives. The glycome was stable upon storage after centrifugation and aliquoting, which is an important information considering future diagnostic applications. Hemolysis, however, negatively correlated with an established glycan score for ovarian cancer, when evaluated by MALDI-TOF-MS measurement by affecting relative intensities of certain glycans, which could lead to false negative / positive results in glycan biomarker studies.

Journal ArticleDOI
TL;DR: It is revealed that FcγRIIIA glycans do impact protein conformation and IgG affinity and display cell-specific glycosylation patterns, leading to a potential model in which the affinity and possibly function of Fc receptors is dictated by the cell type and its surface glycome.

Dissertation
01 Jan 2018
TL;DR: This thesis uses a novel in vitro model of lung adenocarcinoma metastasis to study the changes in cell surface glycosylation that correspond with and may influence metastatic progression, and leverage protein-glycan structural insights to understand and predict the susceptibility of a novel seal influenza virus, H3N8, to infect human populations.
Abstract: Understanding structure-function relationships involved in development of disease is a critical component for the rational design of successful therapeutics, allowing researchers to target precise molecular mechanisms and to anticipate and address future challenges early in development. However, for many diseases and contexts, these precise relationships are unknown or poorly defined. In this thesis, I develop new tools and implement integrated approaches to explore structure-function relationships of disease in two biological contexts: i) the interactions of proteins with glycans that can modify disease susceptibility, and ii) the interactions of viral coat proteins with antibodies that neutralize and prevent viral infection. Section 1: Glycosylation, which is the addition of sugar moieties to proteins and peptides, is one of the most abundant post-translational modifications, modifying a diverse set of biological processes in both health and disease. However, the glycome, or ensemble of glycan structures produced by a cell, is difficult to study, given the low-affinity, high-avidity structural interactions of glycans with host proteins and their non-template-driven biosynthesis. In this section, I investigate how changes in glycomic composition affect disease, and develop and implement tools and approaches that address the aforementioned challenges. In the first part, I leverage a novel in vitro model of lung adenocarcinoma metastasis to study the changes in cell surface glycosylation that correspond with and may influence metastatic progression. Here, I implement and integrate tools, such as glycan biosynthesis gene expression analysis, glycan mass spectrometry analysis frameworks, and lectin binding arrays, to measure the changes in the glycome, identifying several key motifs and glycomic features of metastatic cells. In the second part, I leverage protein-glycan structural insights to understand and predict the susceptibility of a novel seal influenza virus, H3N8, to infect human populations. Here, we used a glycan array, an assay which measures a diversity of glycan binding motifs with biologically relevant avidity and presentation, to demonstrate that unlike human-adapted H3N2, H3N8 lacks the affinity for long a2,6-linked sialylated glycans, which have been shown to determine host specificity and tropism for humans. This result was compared to other experiments, including tissue staining and in vitro replication, to determine that this seal H3N8 virus is unlikely to infect and spread within human populations. These insights further our understanding of how complex ensembles of glycans can influence susceptibility to disease. Section 2: The neutralization of emergent viral pathogens, including Ebola and Zika viruses, by therapeutic antibodies offers the potential to prevent viral infection and to treat patients even after they have been infected. However, given the real-time nature of viral outbreaks, strategies are needed which reduce the development cycle by allowing rational design and selection of potent…

01 Jan 2018
TL;DR: In this paper, Nish Chaturvedi's name was spelt incorrectly in the author list and the details given in this correction are correct. But the authors regret the error.
Abstract: The authors regret that Nish Chaturvedi’s name was spelt incorrectly in the author list. The details given in this correction are correct.

Posted ContentDOI
10 Jul 2018-bioRxiv
TL;DR: A genome-wide association study of the human blood plasma N-glycome composition in up to 3811 people found and replicated twelve loci to demonstrate a clear overlap in genetic control between total plasma and IgG glycosylation.
Abstract: Glycosylation is a common post-translational modification of proteins. It is known, that glycans are directly involved in the pathophysiology of every major disease. Defining genetic factors altering glycosylation may provide a basis for novel approaches to diagnostic and pharmaceutical applications. Here, we report a genome-wide association study of the human blood plasma N-glycome composition in up to 3811 people. We discovered and replicated twelve loci. This allowed us to demonstrate a clear overlap in genetic control between total plasma and IgG glycosylation. Majority of loci contained genes that encode enzymes directly involved in glycosylation (FUT3/FUT6, FUT8, B3GAT1, ST6GAL1, B4GALT1, ST3GAL4, MGAT3, and MGAT5). We, however, also found loci that are likely to reflect other, more complex, aspects of plasma glycosylation process. Functional genomic annotation suggested the role of DERL3, which potentially highlights the role of glycoprotein degradation pathway, and such transcription factor as IKZF1.


Dissertation
01 Sep 2018
TL;DR: A novel inhibition assay for FucT using the fluorogenically labeled disaccharide, MU-β-LacNAc is presented, which shows good potential for high throughput and setting the groundwork for future fully automated screens for potential inhibitors of glycosyltransferases.
Abstract: Cell-surface carbohydrates—or glycans—influence growth, differentiation, and immune response mechanisms. Alterations to the glycome can be markers for diseases including diabetes, neurodegenerative disorders, and cancer. Fucosyltransferases catalyze the addition of a fucose sugar residue to specific cell-surface glycans, which are involved in intercellular cell rolling/adhesion interactions such as white blood cells homing to inflammation sites and sperm-egg binding in fertilization. Fucosylated glycans are also implicated in inflammatory disease and cancers. In viral and microbial infections, fucosyltransferases can play a role in the adhesion and colonization of the host organism, as in the case of Helicobacter pylori α(1,3)-fucosyltransferase (FucT). To better our understanding of glycome alterations and improve medical diagnostics and treatments, screens for glycosyltransferase activity and inhibition are needed. Efficient screens for specific glycosylations tend toward costly materials, instrumentation, and specialized skillsets- here, we present a novel inhibition assay for FucT using the fluorogenically labeled disaccharide, MU-β-LacNAc. The assay shows good potential for high throughput (Z’=0.78 in 384-well plate), though such an application is not shown here. It was also implemented on a digital microfluidic (DMF) platform, where inhibition curves of FucT by GDP, a product of the glycosyltransferase reaction that exhibits an inhibitory feed-back loop, were generated on-device. Results of the assay on DMF (IC50 = 0.093 mM ± 0.037) were shown to be comparable to results in a 384-well plate (IC50 = 0.114 mM ± 0.086), achieving a 87.5% reduction in reaction volume and setting the groundwork for future fully automated screens for potential inhibitors of glycosyltransferases.